BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6013329.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 1,249,229
number of mapped reads = 1,015,350 (81.28%)
number of supplementary alignments = 5,319 (0.43%)
number of secondary alignments = 0
number of mapped bases = 69,289,239 bp
number of sequenced bases = 69,255,303 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 16,882
duplication rate = 1.43%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.3298
>>>>>>> ACTG content
number of A's = 21,269,159 bp (30.71%)
number of C's = 11,531,144 bp (16.65%)
number of T's = 21,163,101 bp (30.56%)
number of G's = 15,264,867 bp (22.04%)
number of N's = 27,032 bp (0.04%)
GC percentage = 38.69%
>>>>>>> Mismatches and indels
general error rate = 0.0113
number of mismatches = 778,564
number of insertions = 4,381
mapped reads with insertion percentage = 0.43%
number of deletions = 19,986
mapped reads with deletion percentage = 1.94%
homopolymer indels = 49.79%
>>>>>>> Coverage
mean coverageData = 0.0224X
std coverageData = 0.181X
There is a 2.03% of reference with a coverageData >= 1X
There is a 0.16% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 5668848 0.022743566203592327 0.23926939563060118
chr2 243199373 9167125 0.03769386773871329 0.2253419352228306
chr3 198022430 4302433 0.02172699830014206 0.1582706587957775
chr4 191154276 4663231 0.024395117376291388 0.16958356871269503
chr5 180915260 3131983 0.017311878500464804 0.14060563276586938
chr6 171115067 3121654 0.01824301071044784 0.1530971206540972
chr7 159138663 4214658 0.026484186309897552 0.22541773863408415
chr8 146364022 4158376 0.028411189738964674 0.2405829502153072
chr9 141213431 2336515 0.01654598279677802 0.14678106390022527
chr10 135534747 3213277 0.023708141794812218 0.18171912950344066
chr11 135006516 2961873 0.02193874109009672 0.17380944011066154
chr12 133851895 3797854 0.028373554218264898 0.18367176921269704
chr13 115169878 1267814 0.011008208240005255 0.11122399396137365
chr14 107349540 2418710 0.02253116315170051 0.16422640625478335
chr15 102531392 1996329 0.019470417411284146 0.1523649603033105
chr16 90354753 2041277 0.022591805436068205 0.1643275216203657
chr17 81195210 1355693 0.016696711542466606 0.14570776074797642
chr18 78077248 1554307 0.01990729744982815 0.20433700137420557
chr19 59128983 912730 0.015436253994086114 0.15107585373146232
chr20 63025520 1423989 0.022593847698519583 0.16257591592723272
chr21 48129895 1338296 0.02780591979267771 0.1849562258175644
chr22 51304566 479942 0.009354761913393829 0.10364494063466813
chrMT 16571 6548 0.39514815038319956 0.7809945008790996
chrX 155270560 3656238 0.023547528906960855 0.16998124970017958
chrY 59373566 99539 0.0016764868055929132 0.045688805919712625